VFDB 2016: hierarchical and refined dataset for big data analysis-10 years on

被引:1166
作者
Chen, Lihong
Zheng, Dandan
Liu, Bo
Yang, Jian [1 ]
Jin, Qi [1 ]
机构
[1] Chinese Acad Med Sci, Inst Pathogen Biol, MOH Key Lab Syst Biol Pathogens, Beijing 100176, Peoples R China
关键词
NEXT-GENERATION; MICROBIOLOGY; UPDATE;
D O I
10.1093/nar/gkv1239
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The virulence factor database (VFDB, http://www.mgc.ac.cn/VFs/) is dedicated to providing up-to-date knowledge of virulence factors (VFs) of various bacterial pathogens. Since its inception the VFDB has served as a comprehensive repository of bacterial VFs for over a decade. The exponential growth in the amount of biological data is challenging to the current database in regard to big data analysis. We recently improved two aspects of the infrastructural dataset of VFDB: (i) removed the redundancy introduced by previous releases and generated two hierarchical datasets - one core dataset of experimentally verified VFs only and another full dataset including all known and predicted VFs and (ii) refined the gene annotation of the core dataset with controlled vocabularies. Our efforts enhanced the data quality of the VFDB and promoted the usability of the database in the big data era for the bioinformatic mining of the explosively growing data regarding bacterial VFs.
引用
收藏
页码:D694 / D697
页数:4
相关论文
共 16 条
[1]   GenBank [J].
Benson, Dennis A. ;
Clark, Karen ;
Karsch-Mizrachi, Ilene ;
Lipman, David J. ;
Ostell, James ;
Sayers, Eric W. .
NUCLEIC ACIDS RESEARCH, 2015, 43 (D1) :D30-D35
[2]   Towards Predictive Models of the Human Gut Microbiome [J].
Bucci, Vanni ;
Xavier, Joao B. .
JOURNAL OF MOLECULAR BIOLOGY, 2014, 426 (23) :3907-3916
[3]   Emerging Technologies for the Clinical Microbiology Laboratory [J].
Buchan, Blake W. ;
Ledeboer, Nathan A. .
CLINICAL MICROBIOLOGY REVIEWS, 2014, 27 (04) :783-822
[4]   VFDB: a reference database for bacterial virulence factors [J].
Chen, LH ;
Yang, J ;
Yu, J ;
Ya, ZJ ;
Sun, LL ;
Shen, Y ;
Jin, Q .
NUCLEIC ACIDS RESEARCH, 2005, 33 :D325-D328
[5]   VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors [J].
Chen, Lihong ;
Xiong, Zhaohui ;
Sun, Lilian ;
Yang, Jian ;
Jin, Qi .
NUCLEIC ACIDS RESEARCH, 2012, 40 (D1) :D641-D645
[6]   Next-generation and whole-genome sequencing in the diagnostic clinical microbiology laboratory [J].
Dunne, W. M., Jr. ;
Westblade, L. F. ;
Ford, B. .
EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES, 2012, 31 (08) :1719-1726
[7]   Microbiology Meets Big Data: The Case of Gut Microbiota-Derived Trimethylamine [J].
Falony, Gwen ;
Vieira-Silva, Sara ;
Raes, Jeroen .
ANNUAL REVIEW OF MICROBIOLOGY, VOL 69, 2015, 69 :305-321
[8]   Big data: The future of biocuration [J].
Howe, Doug ;
Costanzo, Maria ;
Fey, Petra ;
Gojobori, Takashi ;
Hannick, Linda ;
Hide, Winston ;
Hill, David P. ;
Kania, Renate ;
Schaeffer, Mary ;
St Pierre, Susan ;
Twigger, Simon ;
White, Owen ;
Rhee, Seung Yon .
NATURE, 2008, 455 (7209) :47-50
[9]   Recovery of a Medieval Brucella melitensis Genome Using Shotgun Metagenomics [J].
Kay, Gemma L. ;
Sergeant, Martin J. ;
Giuffra, Valentina ;
Bandiera, Pasquale ;
Milanese, Marco ;
Bramanti, Barbara ;
Bianucci, Raffaella ;
Pallen, Mark J. .
MBIO, 2014, 5 (04)
[10]   Longitudinal analysis of microbial interaction between humans and the indoor environment [J].
Lax, Simon ;
Smith, Daniel P. ;
Hampton-Marcell, Jarrad ;
Owens, Sarah M. ;
Handley, Kim M. ;
Scott, Nicole M. ;
Gibbons, Sean M. ;
Larsen, Peter ;
Shogan, Benjamin D. ;
Weiss, Sophie ;
Metcalf, Jessica L. ;
Ursell, Luke K. ;
Vazquez-Baeza, Yoshiki ;
Van Treuren, Will ;
Hasan, Nur A. ;
Gibson, Molly K. ;
Colwell, Rita ;
Dantas, Gautam ;
Knight, Rob ;
Gilbert, Jack A. .
SCIENCE, 2014, 345 (6200) :1048-1052